Contacts of the helix formed by residues 69 - 80 (chain A) in PDB entry 3CWM
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with LYS 69 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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66A LEU 6.0 1.3 - - - -
68A THR* 1.3 83.3 - - - +
70A ALA* 1.3 72.8 + - + +
72A THR* 3.2 10.7 + - - -
73A HIS* 3.2 15.1 + - - -
317A ASP* 3.4 27.3 + - - +
319A SER* 3.5 27.4 + - - +
320A GLY* 4.5 16.1 - - - +
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Residues in contact with ALA 70 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69A LYS* 1.3 77.3 - - + +
71A ASP* 1.3 65.1 + - + +
73A HIS* 3.1 4.8 + - - +
74A ASP* 2.8 41.8 + - - +
317A ASP* 5.0 5.4 - - + +
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Residues in contact with ASP 71 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69A LYS 3.4 0.2 + - - -
70A ALA* 1.3 81.9 - - + +
72A THR* 1.3 57.9 + - - +
74A ASP* 4.5 5.8 - - - +
75A GLU* 2.9 37.6 + - - +
310A LYS* 3.7 28.0 + - + -
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Residues in contact with THR 72 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68A THR* 3.8 19.7 - - + -
69A LYS 3.2 9.9 + - - -
71A ASP* 1.3 77.6 - - - +
73A HIS* 1.3 62.1 + - - +
75A GLU* 3.6 2.8 + - - +
76A ILE* 3.4 24.9 + - - +
310A LYS* 3.5 25.4 - - - +
311A VAL* 3.7 36.0 + - + +
316A ALA* 3.8 2.0 - - + -
317A ASP* 3.0 35.5 + - - +
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Residues in contact with HIS 73 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65A SER* 3.3 31.6 + - - -
68A THR* 3.1 21.4 + - - +
69A LYS* 3.2 17.3 + - - -
70A ALA 3.1 8.9 + - - +
72A THR* 1.3 76.4 - - - +
74A ASP* 1.3 84.4 + - - +
76A ILE* 3.2 16.6 + - - +
77A LEU* 3.4 38.4 + - + +
84A LEU* 4.9 1.3 - - + -
89A GLU* 3.4 39.9 + - - +
93A HIS* 4.9 5.7 + - - -
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Residues in contact with ASP 74 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70A ALA* 2.8 26.6 + - - +
71A ASP* 4.1 6.7 - - - +
73A HIS* 1.3 92.5 + - - +
75A GLU* 1.3 57.3 + - - +
77A LEU* 3.4 0.7 + - - -
78A GLU* 2.9 39.6 + - + +
84A LEU* 3.6 23.9 - - + +
89A GLU* 4.6 2.6 - - - +
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Residues in contact with GLU 75 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71A ASP* 2.9 18.9 + - - +
72A THR 3.7 5.2 - - - +
73A HIS 3.2 0.2 - - - -
74A ASP* 1.3 77.6 - - - +
76A ILE* 1.3 57.5 + - + +
78A GLU* 3.8 5.0 - - - +
79A GLY* 2.8 26.0 + - - -
307A GLY 3.2 22.3 - - - +
308A ILE* 3.6 9.2 - - + +
309A THR* 3.1 17.1 + - - -
310A LYS* 2.8 46.3 + - - +
311A VAL 4.6 0.5 + - - -
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Residues in contact with ILE 76 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61A PHE* 3.3 44.9 - - + +
64A LEU* 4.8 5.2 - - + -
65A SER* 4.3 13.0 - - - +
68A THR* 4.0 29.6 - - + +
72A THR 3.4 17.7 - - - +
73A HIS 3.2 5.5 + - - +
75A GLU* 1.3 77.4 - - + +
77A LEU* 1.3 57.9 + - + +
79A GLY* 3.1 2.9 + - - -
80A LEU* 2.9 36.9 + - + +
308A ILE* 3.8 25.3 - - + +
311A VAL* 4.2 17.7 - - + -
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Residues in contact with LEU 77 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62A ALA* 4.5 6.7 - - + -
65A SER* 3.8 23.6 - - - +
73A HIS* 3.4 39.7 + - + +
74A ASP 3.4 4.5 + - - +
76A ILE* 1.3 73.8 - - - +
78A GLU* 1.3 62.7 + - - +
80A LEU* 3.3 20.7 + - + +
82A PHE* 2.9 41.0 + - + +
84A LEU* 4.0 18.4 - - + -
89A GLU* 4.5 4.7 - - + -
92A ILE* 4.0 35.9 - - + -
93A HIS* 5.0 5.4 - - + +
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Residues in contact with GLU 78 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74A ASP* 2.9 31.3 + - + +
75A GLU* 3.9 4.9 - - - +
77A LEU* 1.3 75.4 - - - +
79A GLY* 1.3 58.6 + - - +
80A LEU 3.1 0.4 - - - -
81A ASN* 3.0 20.6 + - - -
82A PHE 2.9 28.6 + - - +
83A ASN* 4.0 7.8 - - - +
84A LEU* 3.5 31.4 + - + +
85A THR* 5.1 3.3 + - - +
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Residues in contact with GLY 79 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33A PHE* 3.6 19.2 - - - -
75A GLU 2.8 17.8 + - - -
76A ILE 3.1 6.2 + - - -
78A GLU* 1.3 75.8 - - - +
80A LEU* 1.3 56.5 + - - +
81A ASN* 3.2 6.9 + - - -
306A LEU* 4.0 24.2 - - - +
307A GLY 5.3 0.4 - - - -
308A ILE* 3.8 19.5 - - - +
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Residues in contact with LEU 80 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29A ASN* 3.8 9.7 - - - +
30A LEU* 5.4 0.2 - - - -
33A PHE* 3.7 37.1 - - + +
57A ILE* 4.9 0.9 - - + +
58A ALA* 3.7 38.1 - - + +
61A PHE* 4.3 10.1 - - + -
62A ALA* 3.9 15.7 - - + +
76A ILE* 2.9 26.0 + - + +
77A LEU* 3.3 17.9 + - + +
78A GLU 3.1 0.8 - - - -
79A GLY* 1.3 76.9 - - - +
81A ASN* 1.3 71.3 + - - +
82A PHE* 3.4 24.5 - - + -
96A PHE* 4.8 0.7 - - + -
303A LEU* 5.5 0.7 - - + -
308A ILE* 4.7 6.7 - - + -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il